www.rcsb.org Open in urlscan Pro
128.6.159.248  Public Scan

Submitted URL: https://rcsb.org/
Effective URL: https://www.rcsb.org/
Submission: On December 06 via api from US — Scanned from US

Form analysis 1 forms found in the DOM

Name: feedbackfrmPOST

<form id="feedbackfrm" name="feedbackfrm" action="" method="POST">
  <fieldset class="hidden parameters">
    <input id="projectkey" name="projectkey" value="HELP" type="hidden">
    <input id="issuetype" name="issuetype" value="Bug" type="hidden">
  </fieldset>
  <div class="row">
    <!-- NAME -->
    <div class="col-lg-4 col-md-4 col-sm-4 col-xs-12">
      <div id="fname-group" class="form-group">
        <label for="fname">First Name</label>
        <input type="text" class="form-control input-sm reqd" id="fname" name="fname">
      </div>
    </div>
    <div class="col-lg-4 col-md-4 col-sm-4 col-xs-12">
      <div id="lname-group" class="form-group">
        <label for="lname">Last Name</label>
        <input type="text" class="form-control input-sm reqd" id="lname" name="lname">
      </div>
    </div>
    <div class="col-lg-4 col-md-4 col-sm-4 col-xs-12">
      <div id="email-group" class="form-group">
        <label for="email">Email</label>
        <input type="text" class="form-control input-sm reqd" id="email" name="email">
      </div>
    </div>
  </div>
  <!-- ISSUE -->
  <div id="subject-group" class="form-group">
    <label for="subject">Subject</label>
    <input type="text" class="form-control input-sm reqd" id="subject" name="subject">
  </div>
  <div id="description-group" class="form-group">
    <label for="description">Question, Comment, Feedback or Other</label>
    <textarea class="form-control input-sm reqd" id="description" name="description" rows="4"></textarea>
  </div>
  <!-- FILE UPLOAD -->
  <div id="file-group" class="form-group">
    <label for="file">Attach File(s)</label>
    <br>
    <small>Use CTRL or Shift keys to select more than one file (<span id="maxuploads"></span> files max)</small>
    <input type="file" id="file" name="file" class="form-control input-sm" multiple="">
  </div>
  <!-- Privacy Policy -->
  <div class="checkbox">
    <label>
      <input type="checkbox" checked="" name="privacyPolicyAgreement" id="privacyPolicyAgreement"> I agree to the <a href="https://www.rcsb.org/pages/privacy-policy" target="_blank">Help Desk Privacy Policy</a>
    </label>
  </div>
  <!-- OPTIONAL -->
  <hr>
  <label>Optional: To help us learn more about our users, what is your:</label>
  <div class="row">
    <div class="col-lg-4 col-md-4 col-sm-4 col-xs-12">
      <div id="institution-type-group" class="form-group">
        <label for="instype">Institution Type</label>
        <select class="form-control" id="instype">
          <option>College/University</option>
          <option>Research Institute</option>
          <option>Industry</option>
          <option>Non-Profit Organization</option>
          <option>Government</option>
          <option>Hospital</option>
          <option>K12/Primary-Secondary Education</option>
          <option>Other</option>
        </select>
      </div>
    </div>
    <div class="col-lg-4 col-md-4 col-sm-4 col-xs-12">
      <div id="role-group" class="form-group">
        <label for="role">Role</label>
        <select class="form-control" id="role">
          <option>Graduate Student</option>
          <option>Postdoctoral Scholar</option>
          <option>Faculty</option>
          <option>Staff</option>
          <option>Software Developer</option>
          <option>Undergraduate Student</option>
          <option>High School Teacher</option>
          <option>High School Student</option>
          <option>Other</option>
        </select>
      </div>
    </div>
    <div class="col-lg-4 col-md-4 col-sm-4 col-xs-12">
      <div id="rsrch-intrst-group" class="form-group">
        <label for="rsrch-intrst">Main Research Interest</label>
        <select class="form-control" id="rsrch-intrst">
          <option>Biology and Biochemistry</option>
          <option>Molecular Biology and Genetics</option>
          <option>Computer Science</option>
          <option>Chemistry</option>
          <option>Microbiology</option>
          <option>Pharmacology and Toxicology</option>
          <option>Immunology</option>
          <option>Physics</option>
          <option>Clinical Medicine</option>
          <option>Neuroscience and Behavior</option>
          <option>Engineering</option>
          <option>Plant and Animal Science</option>
          <option>Materials Science</option>
          <option>Environment/Ecology</option>
          <option>Mathematics</option>
          <option>Social Sciences, General</option>
          <option>Agricultural Sciences</option>
          <option>Space Science</option>
          <option>Economics and Business</option>
          <option>Geosciences</option>
          <option>Psychiatry/Psychology</option>
          <option>Other</option>
        </select>
      </div>
    </div>
    <div class="modal-footer">
      <button type="button" id="jira-fdbck-close" class="btn btn-default btn-sm" data-dismiss="modal">Close</button>
      <button id="jira-fdbck-submit" type="button" class="btn btn-primary btn-sm">Submit</button>
    </div>
  </div>
</form>

Text Content

Warning You are using a web browser that we do not support. Our website will not
work properly. Please update to a newer version or download a new web browser,
such as Chrome or Firefox.
Help
Contact us
MyPDB
 * Sign in with Google
 * Sign in with Facebook
 * Sign in with ORCID

   --------------------------------------------------------------------------------

 * Help

Toggle navigationRCSB PDB
 * Deposit 
   
      PREPARE DATA
   
    * PDBx/mmCIF file
    * pdb_extract
    * SF-Tool
    * Ligand Expo
    * MAXIT
   
      VALIDATE DATA
   
    * Validation Server
    * Validation API
    * Information for Journals
    * Validation Task Forces
   
      DEPOSIT DATA
   
    * wwPDB OneDep System
    * PDB-Dev
   
      HELP AND RESOURCES
   
    * Deposit FAQ
    * Validation FAQ
    * Tutorials
    * Annotation Policies
    * Processing Procedures
    * PDBx/mmCIF Dictionary
    * PDBx/mmCIF User Guide
    * Chemical Component Dictionary
    * Biologically Interesting Molecule Reference Dictionary (BIRD)
    * BioSync/Beamlines/Facilities
    * Related Tools

 * Search 
   * Advanced Search
   * Sequence Similarity Search
   * Structure Similarity Search
   * Chemical Similarity Search
   * Chemical Sketch Tool
   * Browse by Annotations
   * New Entries
   * Unreleased Entries
   * PDB Statistics
 * Visualize 
   * Mol* (MolStar)
   * Sequence Annotations Viewer
   * Genome View
 * Analyze 
   * Pairwise Structure Alignment
   * Symmetry Resources in the PDB
   * Structure Quality
   * Grouping Structures
   * PDB Citation MeSH Network Explorer
   * PDB Statistics
   * EPPIC Biological Assemblies
   * External Data and Resources
   * Integrated Resources
   * Additional Resources
 * Download 
   * Coordinates and Experimental Data
   * Sequences
   * Ligands
   * File Download Services
   * Web APIs
 * Learn 
   
     
   
   * Training Courses
   * Guide to PDB Data
   * Molecule of the Month
   * Educational Resources
   * Curricula
   * Browse
   * News
   * SciArt Galleries
   * Irving Geis
   * David Goodsell
 * About 
   * Contact Us
   * About RCSB PDB
   * Vision and Mission
   * Citation, Usage, Privacy Policies, Logo
   * News
   * PDB History
   * PDB50
   * User Community
   * Publications
   * RCSB PDB Advisory Committee
   * Team Members
   * Diversity, Equity, Inclusion, and Access
   * Service Status
 * Careers
 * COVID-19
 *  * 
    * 
    * 
    * 
    * 


228,227 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

Include CSM



Advanced Search
|
Browse Annotations
Help

 * 
 * 
 * 
 * 
 * 
 * 

 * 
 * 
 * 
 * 
 * 


  Access Computed Structure Models (CSMs) of available model organismsLearn more
 * Welcome
 * Deposit
 * Search
 * Visualize
 * Analyze
 * Download
 * Learn


WELCOME

RCSB Protein Data Bank (RCSB PDB) enables breakthroughs in science and education
by providing access and tools for exploration, visualization, and analysis of:

Experimentally-determined 3D structures from the Protein Data Bank (PDB) archive



Computed Structure Models (CSM) from AlphaFold DB and ModelArchive

These data can be explored in context of external annotations providing a
structural view of biology.

--------------------------------------------------------------------------------



DECEMBER MOLECULE OF THE MONTH



FLAGELLAR MOTOR


   


   PREPARE DATA

 * PDBX/MMCIF FILE
   
   Prepare data in PDBx/mmCIF format

 * PDB_EXTRACT
   
   Extract data from structure determination programs

 * SF-TOOL
   
   Convert structure factor files among various formats

 * LIGAND EXPO
   
   Search the Chemical Component Dictionary for the IDs of released ligands

 * MAXIT
   
   Translate data between file formats and more

   


   VALIDATE DATA

 * VALIDATION SERVER
   
   Check your X-ray, NMR, or EM structures before depositing-standalone server

 * VALIDATION API
   
   Validate your structures via programmatic remote access before deposition

 * INFORMATION FOR JOURNALS
   
   Instructions to journal editors

 * VALIDATION TASK FORCES
   
   Recommendations from method-specific Validation Task Forces

   


   DEPOSIT DATA

 * WWPDB ONEDEP SYSTEM
   
   Deposit 3D macromolecular structure data to the PDB

 * PDB-DEV
   
   Deposit structural models obtained using integrative hybrid methods

   


   HELP AND RESOURCES

 * Deposit FAQ
 * Validation FAQ
 * Tutorials
 * Annotation Policies
 * Processing Procedures
 * PDBx/mmCIF Dictionary
 * PDBx/mmCIF User Guide
 * Chemical Component Dictionary
 * Biologically Interesting Molecule Reference Dictionary (BIRD)
 * BioSync/Beamlines/Facilities
 * Related Tools



 * ADVANCED SEARCH
   
   Complex boolean queries with values for a wide range of structure attributes

 * SEQUENCE SIMILARITY SEARCH
   
   Find similar protein and nucleic acid sequences using the mmseqs2 method

 * STRUCTURE SIMILARITY SEARCH
   
   Search protein structures by global shape similarity

 * CHEMICAL SIMILARITY SEARCH
   
   Find ligands bound to macromolecules by SMILES String, InChI, or Chemical
   Formula

 * CHEMICAL SKETCH TOOL
   
   Draw a molecule and use the SMILES or InChI string to search for molecules in
   the CCD

 * BROWSE BY ANNOTATIONS
   
   PDB entries in context of annotations by various ontologies and hierarchical
   classification schemes

 * NEW ENTRIES
   
   Search entries released since last Tuesday

 * UNRELEASED ENTRIES
   
   Search entries that are being processed, on hold waiting for release, or have
   been withdrawn

 * PDB STATISTICS
   
   PDB data distribution, archive growth, and more



 * MOL* (MOLSTAR)
   
   3D visualization for PDB structures and ligand binding sites. Access from
   each structure summary page.

 * SEQUENCE ANNOTATIONS VIEWER
   
   Graphical summaries of protein features and their relationships with
   UniProtKB entries. Access from each structure summary page.

 * GENOME VIEW
   
   Graphical summaries of the correspondences between PDB entity sequences and
   genomes. Access from each structure summary page.



 * PAIRWISE STRUCTURE ALIGNMENT
   
   Calculate pairwise structure alignments using various methods

 * SYMMETRY RESOURCES IN THE PDB
   
   Explore tools that display global, local, and helical symmetry among subunits

 * STRUCTURE QUALITY
   
   The slider graphic compares important global quality indicators for a given
   structure with the PDB archive

 * GROUPING STRUCTURES
   
   Explore conservation and trends in the structure properties, features, and
   functions

 * PDB CITATION MESH NETWORK EXPLORER
   
   Find connections between articles describing PDB structures using MeSH terms

 * PDB STATISTICS
   
   PDB data distribution, archive growth, and more

 * EPPIC BIOLOGICAL ASSEMBLIES
   
   EPPIC (Evolutionary Protein-Protein Interface Classifier) finds biological
   interfaces from crystal contacts

 * EXTERNAL DATA AND RESOURCES
   
   
   
   * • Integrated Resources
   * • Additional Resources



 * COORDINATES AND EXPERIMENTAL DATA
   
   Enter PDB IDs to download multiple files in batches containing one or more
   file formats

 * SEQUENCES
   
   Enter PDB IDs to download sequences in FASTA format

 * LIGANDS
   
   Enter the chemical component IDs to download SDF files with ligand
   coordinates

 * FILE DOWNLOAD SERVICES
   
   Download PDB archive or other related data files

 * WEB APIS
   
   The Data API and Search API are the two main APIs that power rcsb.org



Training, Outreach, and Education resources to build and support the broad PDB
user community

 * TRAINING COURSES
   
   Learn to effectively use tools for deposition, searching, analysis, and
   visualization of PDB data

 * GUIDE TO PDB DATA
   
   Guided reference for exploration and interpretation of PDB entries

 * MOLECULE OF THE MONTH
   
   Accounts of selected molecules from the PDB

 * EDUCATIONAL RESOURCES
   
   Resources promoting exploration in the world of proteins and nucleic acids

 * CURRICULA
   
   Authentic, hands-on teaching materials, individual and group activities

 * BROWSE
   
   Browse all PDB-101 resources by biological theme

 * NEWS
   
   Learn about educational offerings and outreach events

 * SCIART GALLERIES
   
   Molecular art for downloading and printing by
   
   * • Irving Geis
   * • David Goodsell





LATEST ENTRIES

As ofTue Dec 03 2024
 1.  
 2.  
 3.  
 4.  
 5.  
 6.  
 7.  
 8.  
 9.  
 10. 


9AY9

--------------------------------------------------------------------------------

CO-CRYSTAL STRUCTURE OF HUMAN PRMT9 IN COMPLEX WITH MRK-990 INHIBITOR


9E8I

--------------------------------------------------------------------------------

HUMAN PROTEASOME IN RESTING STATE CONFORMATION BOUND TO TXNL1 IN FORWARD
CONFORMATION


8XDC

--------------------------------------------------------------------------------

CRYO-EM STRUCTURE OF HUMAN UREA TRANSPORTER A2.


8K52

--------------------------------------------------------------------------------

CRYO-EM STRUCTURE OF CHITIN SYNTHASE


9BCF

--------------------------------------------------------------------------------

CHIMERIC PROTEIN OF CROCODILE ALLERGEN CRO P 1.0101 AND GFP


8Y1S

--------------------------------------------------------------------------------

IN SITU ROOM TEMPERATURE LAUE CRYSTALLOGRAPHY


9J4X

--------------------------------------------------------------------------------

CRYOEM STRUCTURE OF HUMAN XPR1 IN APO STATE


9JIU

--------------------------------------------------------------------------------

FERRITIN MUTANT R63MEHIS


8YWT

--------------------------------------------------------------------------------

THE ISOLATED VO DOMAIN OF V/A-ATPASE FROM THERMUS THERMOPHILUS.


9F08

--------------------------------------------------------------------------------

NUCLEOSIDE-2'-DEOXYRIBOSYLTRANSFERASE FROM LACTOBACILLUS LEICHMANNII. COVALENT
COMPLEX WITH 2-DEOXYRIBOSE.


FEATURES & HIGHLIGHTS

WATCH THE WEBINAR: PYTHON SCRIPTING FOR MOLECULAR DOCKING

This virtual course introduces life scientists to the power and flexibility of
Python Scripting for Molecular Docking

ACCESS SDF/MOL FORMATTED CCD FILES FROM THE PDB ARCHIVE

Chemical Component Dictionary files with ideal geometries in SDF/MOL format are
now available

PAPER PUBLISHED: USING AUGMENTED REALITY

Read about Using augmented reality in molecular case studies to enhance
biomolecular structure-function explorations in undergraduate classrooms

DEVELOPERS: SWITCH TO SEQUENCE COORDINATES SERVICE BY MAY 31, 2025

The new Sequence Coordinates Service supports better access to RCSB PDB features

TAKE THE VISUALIZATION USER SURVEY AND WIN

Please take this brief survey and be entered into a drawing for a mug featuring
the artwork of David S. Goodsell.

DEPRECATION OF FTP FILE DOWNLOAD PROTOCOL ON NOVEMBER 1, 2024

wwPDB to deprecate FTP download protocol in the PDB archive

POSTER PRIZE AWARDED AT THE PROTEIN SOCIETY

The wwPDB Foundation made an award to Aubrey Putansu at The Protein Society
meeting for An Expanded Integrator Sensor Motif for GPCR Ligand Detection

REGISTER FOR UPCOMING TRAINING EVENTS

Join us for free upcoming virtual events: Mol* Office Hour (Nov 4), BCIF Webinar
(Nov 4), and Extended PDB ID Office Hour (Nov 9)

POSTER PRIZE AWARDED AT LACA

The wwPDB Foundation awarded Zaighum Abbas at the Latin American
Crystallographic Association Meeting for The Role of SEPT7 in Magnaporthe
oryzae: Structural Insights and Functional Implications

THE NOBEL PRIZE IN CHEMISTRY 2024

Congratulations to David Baker, who was recognized for computational protein
design, and to Demis Hassabis and John M. Jumper, who were recognized for
protein structure prediction. These achievements also celebrate the work of the
PDB depositor community and the PDB archive that underpinned development of
their prediction methods.


See new feature archive


 * NEWS


 * PUBLICATIONS
   
   * Published in Journals & Books
   
     --------------------------------------------------------------------------------
   
   * Molecule of the Month
   
     --------------------------------------------------------------------------------
   
   * Quarterly Newsletter
   * Annual Report
     

 * STRUCTURAL BIOLOGY AND NOBEL PRIZES
   
   On December 10, the Noel Prize in Chemistry will be awarded to David Baker
   for computational protein design and to Demis Hassabis and John M. Jumper for
   protein structure prediction. Learn more about the PDB and protein
   prediction/design at PDB-101
   » 12/06/2024
   

 * DECEMBER 1: WORLD AIDS DAY
   
   Watch the documentary Target Zero to learn about the challenge and emotional
   complexity of the fight to control HIV infection
   » 11/27/2024
   

 * EDUCATION CORNER: PAPER NUCLEIC ACID MODELS FOR HANDS-ON EDUCATION
   
   Cassandra Hayne and Phoebe Rice (The University of Chicago) describe
   downloadable Paper Nucleic Acid Models for Hands-on Education
   » 11/25/2024
   

 * PDB-101 FOCUS: PEAK PERFORMANCE
   
   PDB-101 materials explore the structural biology of athletics and well-being.
   Learn about the molecular switch that responds to changing oxygen levels in
   Hypoxia-Inducible Factors
   » 11/21/2024
   

 * NOV 18-24: WORLD ANTIMICROBIAL AWARENESS WEEK
   
   PDB structures help us understand resistance to antibiotics and develop new
   ways to fight infection
   » 11/17/2024
   

 * NOV 17: WHO'S CERVICAL CANCER ELIMINATION DAY OF ACTION
   
   Visit PDB-101 to learn how the capsid protein of papillomavirus is used in
   vaccines that prevent cervical cancer
   » 11/14/2024
   

 * NOVEMBER 14 IS WORLD DIABETES DAY
   
   PDB structures reveal how glucose levels are regulated in the body and
   provide new hope for combating the disease.
   » 11/13/2024
   

 * MEET RCSB PDB AT ABRCMS
   
   Visit the poster Streamlining Programmatic Access to Structural Biology Data
   with Python to learn about recent software development; meet Rutgers members
   in booth #1740 to learn about the summer internships and gap year
   opportunities
   » 11/10/2024
   

 * PAPER PUBLISHED: IHMCIF
   
   Read about An Extension of the PDBx/mmCIF Data Standard for Integrative
   Structure Determination Methods
   » 11/05/2024
   

 * MEET RCSB PDB AT SACNAS
   
   Learn about summer internship opportunities and more at the Rutgers booth
   #648
   » 10/27/2024
   


MOLECULE OF THE MONTH

FLAGELLAR MOTOR

Bidirectional motors power the swimming of many bacterial cells.

Read More


QUARTERLY NEWS (SEE ARCHIVE)

ISSUE 103 - OCTOBER 2024

In this Issue: Fall Training Opportunities; A Biocurator Milestone of >10,000
Depositions Processed; Influenza Virus painting; and more.

Education Corner: Paper Nucleic Acid Models for Hands-on Education by Cassandra
K. Hayne and Phoebe A. Rice, The University of Chicago

 * Summer 2024 Issue
 * Spring 2024 Issue
 * Winter 2024 Issue




ANNUAL REPORTS

2023 ANNUAL REPORT

Download the 2023 Annual Report (PDF) for an overview of recent activities,
including RCSB PDB APIs and pairwise alignment tools.

Annual Report Archive


PDB at a Glance
71,478
Structures of Human Sequences
18,631
Nucleic Acid Containing Structures
CSM at a Glance
999,251
AlphaFoldDB
69,326
ModelArchive
More Statistics
 * About
 * About Us
 * Citing Us
 * Publications
 * Team
 * Careers
 * Usage & Privacy

 * Support
 * Contact Us
 * Help
 * Website FAQ
 * Glossary
 * Service Status



RCSB PDB is hosted by

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------

RCSB PDB is a member of the

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------

 * RCSB Partners
 * Nucleic Acid Knowledgebase

 * wwPDB Partners
 * RCSB PDB
 * PDBe
 * PDBj
 * BMRB
 * EMDB

RCSB PDB Core Operations are funded by the U.S. National Science Foundation
(DBI-2321666), the US Department of Energy (DE-SC0019749), and the National
Cancer Institute, National Institute of Allergy and Infectious Diseases, and
National Institute of General Medical Sciences of the National Institutes of
Health under grant R01GM157729.

×


All questions and comments will receive a response in a timely manner.

 * Use this form for questions about RCSB.org and RCSB PDB services.
   Please attach a screenshot when reporting an issue, if possible.
 * To update/release your in-progress structure depositions:
   access the OneDep Communication panel
 * For questions/corrections to specific PDB entries, including citation
   updates:
   email deposit-help@mail.wwpdb.org

First Name
Last Name
Email
Subject
Question, Comment, Feedback or Other
Attach File(s)
Use CTRL or Shift keys to select more than one file ( files max)
I agree to the Help Desk Privacy Policy

--------------------------------------------------------------------------------

Optional: To help us learn more about our users, what is your:
Institution Type College/University Research Institute Industry Non-Profit
Organization Government Hospital K12/Primary-Secondary Education Other
Role Graduate Student Postdoctoral Scholar Faculty Staff Software Developer
Undergraduate Student High School Teacher High School Student Other
Main Research Interest Biology and Biochemistry Molecular Biology and Genetics
Computer Science Chemistry Microbiology Pharmacology and Toxicology Immunology
Physics Clinical Medicine Neuroscience and Behavior Engineering Plant and Animal
Science Materials Science Environment/Ecology Mathematics Social Sciences,
General Agricultural Sciences Space Science Economics and Business Geosciences
Psychiatry/Psychology Other
Close Submit
×


Thank you for providing your feedback! Someone will be in touch with you
shortly. This window will automatically close in 5 seconds.
×


Apologies, our feedback server is currently unavailable and we are
troubleshooting the issue. In the meantime, please copy and paste the below
information into an email addressed to info@rcsb.org